use cmake WITH_MOD_ * to exclude include paths which are not used.

source/blender/blenkernel/CMakeLists.txt

@@ -38,15 +38,11 @@ set(INC
 	../modifiers
 	../nodes
 	../render/extern/include
-	../../../intern/bsp/extern
-	../../../intern/decimation/extern
-	../../../intern/elbeem/extern
 	../../../intern/guardedalloc
 	../../../intern/iksolver/extern
 	../../../intern/memutil
 	../../../intern/mikktspace
 	../../../intern/opennl/extern
-	../../../intern/smoke/extern
 
 	# XXX - BAD LEVEL CALL WM_api.h
 	../windowmanager
@@ -333,10 +329,16 @@ if(WITH_OPENMP)
 endif()
 
 if(WITH_MOD_FLUID)
+	list(APPEND INC
+		../../../intern/elbeem/extern
+	)
 	add_definitions(-DWITH_MOD_FLUID)
 endif()
 
 if(WITH_MOD_SMOKE)
+	list(APPEND INC
+		../../../intern/smoke/extern
+	)
 	add_definitions(-DWITH_SMOKE)
 endif()
 
@@ -344,6 +346,18 @@ if(WITH_MOD_OCEANSIM)
 	add_definitions(-DWITH_OCEANSIM)
 endif()
 
+if(WITH_MOD_DECIMATE)
+	list(APPEND INC
+		../../../intern/decimation/extern
+	)
+endif()
+
+if(WITH_MOD_BOOLEAN)
+	list(APPEND INC
+		../../../intern/bsp/extern
+	)
+endif()
+
 if(WITH_JACK)
 	add_definitions(-DWITH_JACK)
 endif()

source/blender/blenkernel/intern/fluidsim.c

@@ -30,7 +30,11 @@
  */
 
 
-#include <stddef.h>
+// headers for fluidsim bobj meshes
+#include <stdlib.h>
+#include <zlib.h>
+#include <string.h>
+#include <stdio.h>
 
 #include "MEM_guardedalloc.h"
 
@@ -54,14 +58,6 @@
 #include "BKE_modifier.h"
 #include "BKE_mesh.h"
 
-
-// headers for fluidsim bobj meshes
-#include <stdlib.h>
-#include "LBM_fluidsim.h"
-#include <zlib.h>
-#include <string.h>
-#include <stdio.h>
-
 /* ************************* fluidsim bobj file handling **************************** */
 
 

source/blender/blenkernel/intern/object.c

@@ -103,7 +103,9 @@
 #include "BKE_material.h"
 #include "BKE_camera.h"
 
+#ifdef WITH_MOD_FLUID
 #include "LBM_fluidsim.h"
+#endif
 
 #ifdef WITH_PYTHON
 #include "BPY_extern.h"

source/blender/blenkernel/intern/pointcache.c

@@ -74,7 +74,9 @@
 #include "BIK_api.h"
 
 /* both in intern */
+#ifdef WITH_MOD_SMOKE
 #include "smoke_API.h"
+#endif
 
 #ifdef WITH_LZO
 #include "minilzo.h"

source/blender/blenkernel/intern/smoke.c

@@ -73,8 +73,6 @@
 #include "DNA_scene_types.h"
 #include "DNA_smoke_types.h"
 
-#include "smoke_API.h"
-
 #include "BKE_smoke.h"
 
 /* UNUSED so far, may be enabled later */
@@ -82,6 +80,8 @@
 
 #ifdef WITH_SMOKE
 
+#include "smoke_API.h"
+
 #ifdef _WIN32
 #include <time.h>
 #include <stdio.h>